NPASS Compound

Natural Product: NPC600888

The Chemical Classification was calculated by Classyfire, a software for chemical taxonomy calculation. Reference: DOI:10.1186/s13321-016-0174-y.

Chemical Representations

RDKit 3D 61 66 0 0 0 0 0 0 0 0999 V2000 4.5300 -4.8945 0.4778 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1546 -3.7846 1.0453 O 0 0 0 0 0 0 0 0 0 0 0 0 4.6493 -2.4827 0.8608 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5092 -2.2880 0.1020 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0146 -1.0188 -0.0792 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6124 0.0950 0.4705 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0687 1.4366 0.2647 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6295 2.5738 0.7927 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0889 3.8439 0.5802 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5903 4.8729 1.0538 O 0 0 0 0 0 0 0 0 0 0 0 0 1.9523 3.9183 -0.1918 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3294 5.1201 -0.4694 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8877 6.2732 0.0589 O 0 0 0 0 0 0 0 0 0 0 0 0 0.1911 5.1577 -1.2471 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3468 3.9752 -1.7651 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4908 3.9840 -2.5504 O 0 0 0 0 0 0 0 0 0 0 0 0 0.2627 2.7847 -1.4953 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2484 1.5406 -2.0026 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1655 0.8290 -1.2592 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6974 -0.3797 -1.6935 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6730 -1.1025 -0.8658 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2319 -2.2993 -1.2422 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1552 -2.9887 -0.4646 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6533 -4.0776 -0.8243 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.5054 -2.4149 0.7379 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4182 -3.0470 1.5603 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9542 -4.2516 1.1377 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.7422 -2.4411 2.7546 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1662 -1.2279 3.1204 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4806 -0.6023 4.3201 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.2624 -0.6266 2.2795 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9121 -1.2142 1.0617 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0519 -0.6065 0.2999 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.2728 -0.8496 -2.9069 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3385 -0.1254 -3.6650 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1817 1.0704 -3.2254 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1104 1.7825 -3.9874 O 0 0 0 0 0 0 0 0 0 0 0 0 1.4114 2.7553 -0.7094 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9717 1.6025 -0.4686 O 0 0 0 0 0 0 0 0 0 0 0 0 4.7342 -0.1068 1.2158 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2636 -1.3888 1.4193 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6031 -5.2068 1.0019 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2789 -4.7279 -0.5725 H 0 0 0 0 0 0 0 0 0 0 0 0 5.2221 -5.7612 0.5153 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0169 -3.1419 -0.3427 H 0 0 0 0 0 0 0 0 0 0 0 0 2.1302 -0.8877 -0.6702 H 0 0 0 0 0 0 0 0 0 0 0 0 4.5232 2.5263 1.4011 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4266 6.8976 -0.5126 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2843 6.0952 -1.4565 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1781 4.7240 -2.5220 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5237 1.1768 -0.2883 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9724 -2.7655 -2.1778 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.6676 -4.2570 0.4093 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.4512 -2.9142 3.4129 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.9054 0.3268 4.2831 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8257 0.3211 2.5874 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6568 -1.7886 -3.2924 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0181 -0.5148 -4.6184 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5160 1.3099 -4.7849 H 0 0 0 0 0 0 0 0 0 0 0 0 5.2472 0.7229 1.6717 H 0 0 0 0 0 0 0 0 0 0 0 0 6.1418 -1.5314 2.0046 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 2 0 4 5 1 0 5 6 2 0 6 7 1 0 7 8 2 0 8 9 1 0 9 10 2 0 9 11 1 0 11 12 2 0 12 13 1 0 12 14 1 0 14 15 2 0 15 16 1 0 15 17 1 0 17 18 1 0 18 19 2 0 19 20 1 0 20 21 1 0 21 22 2 0 22 23 1 0 23 24 2 0 23 25 1 0 25 26 2 0 26 27 1 0 26 28 1 0 28 29 2 0 29 30 1 0 29 31 1 0 31 32 2 0 32 33 1 0 20 34 2 0 34 35 1 0 35 36 2 0 36 37 1 0 17 38 2 0 38 39 1 0 6 40 1 0 40 41 2 0 41 3 1 0 39 7 1 0 38 11 1 0 36 18 1 0 33 21 1 0 32 25 1 0 1 42 1 0 1 43 1 0 1 44 1 0 4 45 1 0 5 46 1 0 8 47 1 0 13 48 1 0 14 49 1 0 16 50 1 0 19 51 1 0 22 52 1 0 27 53 1 0 28 54 1 0 30 55 1 0 31 56 1 0 34 57 1 0 35 58 1 0 37 59 1 0 40 60 1 0 41 61 1 0 M END

Calculated Properties

Physi-Chem Properties

MedChem Properties

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

ADMET: Distribution

ADMET: Metabolism

ADMET: Excretion

ADMET: Toxicity

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference

Note for Reference:
In addition to directly collecting NP source organism data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated them from below databases:
☉ UNPD: Universal Natural Products Database [PMID: 23638153].
☉ StreptomeDB: a database of streptomycetes natural products [PMID: 33051671].
☉ TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine [PMID: 26156871].
☉ TCM@Taiwan: a Traditional Chinese Medicine database [PMID: 21253603].
☉ TCMID: a Traditional Chinese Medicine database [PMID: 29106634].
☉ TCMSP: The traditional Chinese medicine systems pharmacology database and analysis platform [PMID: 24735618].
☉ HerDing: a herb recommendation system to treat diseases using genes and chemicals [PMID: 26980517].
☉ MetaboLights: a metabolomics database [PMID: 27010336].
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

NP Quantity Composition/Concentration

Organism ID	Organism Name	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference

Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP quantitative records for specific NP domains (e.g., NPS from foods or herbs) from domain-specific databases. These databases include:
☉ DUKE: Dr. Duke's Phytochemical and Ethnobotanical Databases.
☉ PHENOL EXPLORER: is the first comprehensive database on polyphenol content in foods [PMID: 24103452], its homepage can be accessed at here.
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

Biological Activity

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

In vitro activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

In vivo activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

Experimental ADME

Experiment Model	Experiment Tissue	ADME Type	ADME Relation	ADME Value	ADME Unit	Reference

Experimental Toxicity

Quantitative toxicity

Experiment Model	Experiment Organism	Toxicity Type	Toxicity Relation	Toxicity Value	Toxicity Unit	Reference

Common Abbreviations:
LC: Lethal Concentration; LD: Lethal Dose; LT:Lethal Time; NOAEL: No-observed-adverse-effect Level; BMDL: Benchmark Dose Lower Confidence Limit; BMD: Benchmark Dose; BMC:Benchmark Concentration; LOAEL: Lowest Observed Adverse Effect Level; RfD:Reference Dose; RfC:Reference Concentration; MRL: Minimal Risk Level; MEG: Maximum Exposure Guideline; PAC: Protective Action Criteria

Categorical toxicity labels

Hepatotoxicity	Carcinogenicity	Mutagenicity	Cardiotoxicity	Respiratory Toxicity	Eye Irritation	Endocrine Disruption

Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP toxicity records from domain-specific databases. These databases include:
☉ ToxValDB: a curated database that compiles quantitative toxicity values for chemicals from diverse public sources to support toxicological research and risk assessment.
☉ TOXRIC: a comprehensive, free-to-access, online database providing toxicological/feature data. The toxicity labels are retrieved from this database. [PMID: 36400569]

Chemically structural similarity

Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes approximately 50,000 NPs with experimentally-derived bioactivity available in NPASS)

Similarity is measured using the Tanimoto coefficient (Tc) , which compares the binary fingerprints of two molecules. Tc is calculated as the intersection divided by the union of '1' bits in the fingerprints, ranging from 0 to 1, with 1 indicating highest similarity.

● The left chart: Distribution of similarity level between NPC600888 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	30287
0.1-0.2	16763
0.2-0.3	1835
0.3-0.4	746
0.4-0.5	156
0.5-0.6	40
0.6-0.7	16
0.7-0.8	0
0.8-0.85	4
0.85-0.9	0
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC303485
0.8261	Intermediate Similarity	NPC121649
0.8143	Intermediate Similarity	NPC601565
0.8125	Intermediate Similarity	NPC138299
0.8088	Intermediate Similarity	NPC150908
0.7714	Intermediate Similarity	NPC71061
0.7606	Intermediate Similarity	NPC194593
0.7419	Intermediate Similarity	NPC231772
0.7222	Intermediate Similarity	NPC290830
0.6892	Remote Similarity	NPC186227
0.6806	Remote Similarity	NPC259757
0.6667	Remote Similarity	NPC14606
0.6667	Remote Similarity	NPC610480
0.6623	Remote Similarity	NPC265624
0.6622	Remote Similarity	NPC600972
0.6579	Remote Similarity	NPC215203
0.6533	Remote Similarity	NPC72425
0.6533	Remote Similarity	NPC158027
0.6338	Remote Similarity	NPC111112
0.6324	Remote Similarity	NPC12200
0.6232	Remote Similarity	NPC183950
0.6087	Remote Similarity	NPC52005
0.6081	Remote Similarity	NPC254351
0.6076	Remote Similarity	NPC18699
0.6049	Remote Similarity	NPC55443
0.5974	Remote Similarity	NPC603508
0.5938	Remote Similarity	NPC50898
0.5915	Remote Similarity	NPC67322
0.5882	Remote Similarity	NPC483773
0.5867	Remote Similarity	NPC183
0.5846	Remote Similarity	NPC222713
0.5811	Remote Similarity	NPC291746
0.5811	Remote Similarity	NPC288840
0.5775	Remote Similarity	NPC610914
0.5652	Remote Similarity	NPC62536
0.5652	Remote Similarity	NPC120464
0.5652	Remote Similarity	NPC601901
0.5625	Remote Similarity	NPC272064
0.5616	Remote Similarity	NPC605634
0.56	Remote Similarity	NPC112954
0.5522	Remote Similarity	NPC279121
0.5507	Remote Similarity	NPC52611
0.5507	Remote Similarity	NPC156222
0.5507	Remote Similarity	NPC29353
0.5488	Remote Similarity	NPC205026
0.5455	Remote Similarity	NPC78540
0.5455	Remote Similarity	NPC196179
0.5443	Remote Similarity	NPC248739
0.5432	Remote Similarity	NPC159707
0.5429	Remote Similarity	NPC184136
0.5429	Remote Similarity	NPC59951
0.5429	Remote Similarity	NPC241838
0.5429	Remote Similarity	NPC266597
0.5417	Remote Similarity	NPC606638
0.5385	Remote Similarity	NPC603692
0.5375	Remote Similarity	NPC601984
0.5366	Remote Similarity	NPC143851
0.5352	Remote Similarity	NPC603662
0.5286	Remote Similarity	NPC600177
0.5256	Remote Similarity	NPC34089
0.5211	Remote Similarity	NPC234133
0.5139	Remote Similarity	NPC600900
0.5125	Remote Similarity	NPC606549
0.5072	Remote Similarity	NPC274121
0.507	Remote Similarity	NPC241498

Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

● The left chart: Distribution of similarity level between NPC600888 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	5887
0.1-0.2	3202
0.2-0.3	50
0.3-0.4	8
0.4-0.5	2
0.5-0.6	1
0.6-0.7	0
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.5522	Remote Similarity	NPD1511	Phase 2

Bioactivity similarity

Similar Natural Products in NPASS

Similarity level is defined by Bioactivity similarity was calculated based on bioactivity descriptors of compounds. The bioactivity descriptors were calculated by a recently developed AI algorithm Chemical Checker (CC) [Nature Biotechnology, 38:1087–1096, 2020; Nature Communications, 12:3932, 2021], which evaluated bioactivity similarities at five levels:
☉ A: chemistry similarity;
☉ B: biological targets similarity;
☉ C: networks similarity;
☉ D: cell-based bioactivity similarity;
☉ E: similarity based on clinical data.
Those 5 categories of CC bioactivity descriptors were calculated and then subjected to manifold projection using UMAP algorithm, to project all NPs on a 2-Dimensional space. The current NP was highlighted with a small circle in the 2-D map. Below figures: left-to-right, A-to-E.

A: chemistry similarity

B: biological targets similarity

C: networks similarity

D: cell-based bioactivity similarity

E: similarity based on clinical data